Home About us Contact
|
Home About us Contact | ||
|
|
||
Molecular Network (molecular + network)
Selected AbstractsSteering Two-Dimensional Molecular Growth via Dipolar InteractionCHEMPHYSCHEM, Issue 12 2009Stefan Kuck Molecular networks: Chiral and metallized Salen molecules on a Cu(111) are investigated using local probe techniques (see figure). Whereas for the parent Co-Salen molecule no self-assembly is observed, in the metal,organic complexes the growth of large and regular molecular networks is achieved through a target-oriented synthetic design of the local electrostatic dipolar molecular fields. [source] Molecular magnetism via resonating valence bonds for conjugated radicals and selected transition metal complexesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 4-5 2001D. J. Klein Abstract Currently there is considerable interest in the nature of exchange interactions leading to unpaired electrons in molecular and cluster magnets. Here, the focus is largely at a qualitative level, via a novel "mean-field" resonance-theoretic view, to deal with exchange couplings, so as to allow unpaired electrons in either (or both of) the ,- and ,-parts of a (largely organic) bipartite (or alternate) molecular network. The (quantitative) number and (qualitative) location of unpaired spins are dealt with by this simple approach, which also offers some (qualitative) information on the occurrence of low-lying higher-spin states. To illustrate the approach it is applied to a variety of systems where the spin sources are conjugated ,-network molecules and polymers, carbenes, variously defected graphites, and a few species involving transition metals, especially Cu. The discussion deals not only with traditional conjugated organics compounds but also with selected inorganic species. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001 [source] Decorin and its galactosaminoglycan chain: Extracellular regulator of cellular function?IUBMB LIFE, Issue 11 2008Daniela G. Seidler Abstract A molecular network of extracellular matrix molecules determines the tissue architecture and accounts for mechanical properties like compressibility or stretch resistance. It is widely accepted that the elements of the cellular microenvironment are important regulators of the cellular behavior in vitro and in vivo. One large group comprising these molecules is the family of proteoglycans. Both, the core proteins and, in particular, the attached galactosaminoglycans, contribute to the regulation network as they bind a variety of signaling molecules, e.g. cytokines, chemokines, growth, and differentiation factors. We would like to emphasize specific patterns of epimerization and sulfation within the galactosaminoglycans chains, because these result in "motifs" that are responsible for the modulation of signal factor binding, release and activity. This property is crucial in physiological and pathological conditions, for example development and wound healing. © 2008 IUBMB IUBMB Life, 60(11): 729,733, 2008 [source] Localization of synaptic proteins involved in neurosecretion in different membrane microdomainsJOURNAL OF NEUROCHEMISTRY, Issue 3 2007Elena Taverna Abstract A number of proteins and signalling molecules modulate voltage-gated calcium channel activity and neurosecretion. As recent findings have indicated the presence of Cav2.1 (P/Q-type) channels and soluble N -ethyl-maleimide-sensitive fusion protein attachment protein receptors (SNAREs) in the cholesterol-enriched microdomains of neuroendocrine and neuronal cells, we investigated whether molecules known to modulate neurosecretion, such as the heterotrimeric G proteins and neuronal calcium sensor-1 (NCS-1), are also localized in these microdomains. After immuno-isolation, flotation gradients from Triton X-100-treated synaptosomal membranes revealed the presence of different detergent-resistant membranes (DRMs) containing proteins of the exocytic machinery (Cav2.1 channels and SNAREs) or NCS-1; both DRM subtypes contained aliquots of heterotrimeric G protein subunits and phosphatidylinositol-4,5-bisphosphate. In line with the biochemical data, confocal imaging of immunolabelled membrane sheets revealed the localization of SNARE proteins and NCS-1 in different dot-like structures. This distribution was largely impaired by treatment with methyl-,-cyclodextrin, thus suggesting the localization of all three proteins in cholesterol-dependent domains. Finally, bradykinin (which is known to activate the NCS-1 pathway) caused a significant increase in NCS-1 in the DRMs. These findings suggest that different membrane microdomains are involved in the spatial organization of the complex molecular network that converges on calcium channels and the secretory machinery. [source] Neuromyelitis optica/Devic's disease: Gene expression profiling of brain lesionsNEUROPATHOLOGY, Issue 6 2008Jun-ichi Satoh Neuromyelitis optica (NMO), also known as Devic's disease, is an inflammatory demyelinating disease that affects selectively the optic nerves and the spinal cord, possibly mediated by an immune mechanism distinct from that of multiple sclerosis (MS). Recent studies indicate that NMO also involves the brain. Here, we studied gene expression profile of brain lesions of a patient with NMO by using DNA microarray, along with gene expression profile of the brains of Parkinson disease and amyotrophic lateral sclerosis patients. We identified more than 200 genes up-regulated in NMO brain lesions. The top 20 genes were composed of the molecules closely associated with immune regulation, among which marked up-regulation of interferon gamma-inducible protein 30 (IFI30), CD163, and secreted phosphoprotein 1 (SPP1, osteopontin) was validated by real time RT-PCR, Northern blot and Western blot analysis. Pathologically, CD68+ macrophages and microglia expressed intense immunoreactivities for IFI30 and CD163 in NMO lesions, consisting of inflammatory demyelination, axonal loss, necrosis, cavity formation, and vascular fibrosis. KeyMolnet, a bioinformatics tool for analyzing molecular interaction on the curated knowledge database, suggested that the molecular network of up-regulated genes in NMO brain lesions involves transcriptional regulation by the nuclear factor-kappaB (NF-,B) and B-lymphocyte-induced maturation protein-1 (Blimp-1). These results suggest that profound activation of the macrophage-mediated proinflammatory immune mechanism plays a pivotal role in development of NMO brain lesions. [source] Caenorhabditis elegans proteomics comes of agePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2010Yhong-Hee Shim Abstract Caenorhabditis elegans, a free-living soil nematode, is an ideal model system for studying various physiological problems relevant to human diseases. Despite its short history, C. elegans proteomics is receiving great attention in multiple research areas, including the genome annotation, major signaling pathways (e.g. TGF-, and insulin/IGF-1 signaling), verification of RNA interference-mediated gene targeting, aging, disease models, as well as peptidomic analysis of neuropeptides involved in behavior and locomotion. For example, a proteome-wide profiling of developmental and aging processes not only provides basic information necessary for constructing a molecular network, but also identifies important target proteins for chemical modulation. Although C. elegans has a simple body system and neural circuitry, it exhibits very complicated functions ranging from feeding to locomotion. Investigation of these functions through proteomic analysis of various C. elegans neuropeptides, some of which are not found in the predicted genome sequence, would open a new field of peptidomics. Given the importance of nematode infection in plants and mammalian pathogenesis pathways, proteomics could be applied to investigate the molecular mechanisms underlying plant, or animal,nematode pathogenesis and to identify novel antinematodal drugs. Thus, C. elegans proteomics, in combination of other molecular, biological and genetic techniques, would provide a versatile new tool box for the systematic analysis of gene functions throughout the entire life cycle of this nematode. [source] Proteomic analysis identified N-cadherin, clusterin, and HSP27 as mediators of SPARC (secreted protein, acidic and rich in cysteines) activity in melanoma cellsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 22 2007Marķa Soledad Sosa Abstract Secreted protein, acidic and rich in cysteines (SPARC) is a secreted protein associated with increased aggressiveness of different human cancer types. In order to identify downstream mediators of SPARC activity, we performed a 2-DE proteomic analysis of human melanoma cells following antisense-mediated downregulation of SPARC expression. We found 23/504 differential spots, 15 of which were identified by peptide fingerprinting analysis. Three of the differential proteins (N-cadherin (N-CAD), clusterin (CLU), and HSP27) were validated by immunoblotting, confirming decreased levels of N-CAD and CLU and increased amounts of HSP27 in conditioned media of cells with diminished SPARC expression. Furthermore, transient knock down of SPARC expression in melanoma cells following adenoviral-mediated transfer of antisense RNA confirmed these changes. We next developed two different RNAs against SPARC that were able to inhibit in vivo melanoma cell growth. Immunoblotting of the secreted fraction of RNAi-transfected melanoma cells confirmed that downregulation of SPARC expression promoted decreased levels of N-CAD and CLU and increased secretion of HSP27. Transient re-expression of SPARC in SPARC-downregulated cells reverted extracellular N-CAD, CLU, and HSP27 to levels similar to those in the control. These results constitute the first evidence that SPARC, N-CAD, CLU, and HSP27 converge in a unique molecular network in melanoma cells. [source] Regulation of ADL6 activity by its associated molecular networkTHE PLANT JOURNAL, Issue 5 2002Bernard C.-H. Summary Plant dynamin-like proteins consist of a group of high molecular weight GTPase with diverse structural arrangements and cellular localizations. In addition, unlike animal dynamins, there was no evidence for the involvement of any plant dynamin-like protein in clathrin-mediated vesicle trafficking. In this study we demonstrate that ADL6 (Arabidopsis dynamin-like protein 6), due to its domain arrangement, behaves similarly to the animal dynamins. The association of ADL6 with clathrin-coated vesicles was demonstrated by co-fractionation and immunocytochemical studies. ADL6 also interacted via its C-terminus with ,-adaptin, an adaptor protein of clathrin-coated vesicles. Our results suggest that ADL6 participates in clathrin-mediated vesicle trafficking originating from the Golgi. In addition, our studies demonstrate that ADL6 intrinsic GTPase activity is regulated by its association with acidic phospholipids and an SH3 (Src homology 3)-containing protein. [source] Screening of chondrogenic factors with a real-time fluorescence-monitoring cell line ATDC5-C2ER: Identification of sorting nexin 19 as a novel factorARTHRITIS & RHEUMATISM, Issue 11 2009Akinori Kan Objective To establish a cell culture system for noninvasive and real-time monitoring of chondrogenic differentiation in order to screen for chondrogenic factors. Methods The optimum reporter construct transfected into chondrogenic ATDC5 cells was selected by a luciferase reporter assay and fluorescence analysis during cultures with insulin. The established cell line was validated according to its fluorescence following stimulation with SOX proteins, bone morphogenetic protein 2 (BMP-2), or transforming growth factor , (TGF,) and was compared with the level of messenger RNA for COL2A1 as well as with the degree of Alcian blue staining. Screening of chondrogenic factors was performed by expression cloning using a retroviral expression library prepared from human tracheal cartilage. The expression pattern of the identified molecule was examined by in situ hybridization and immunohistochemistry. Functional analysis was performed by transfection of the identified gene, the small interfering RNA, and the mutated gene. Results We established an ATDC5 cell line with 4 repeats of a highly conserved enhancer ligated to a COL2A1 basal promoter and the DsRed2 reporter (ATDC5-C2ER). Fluorescence was induced under the stimulations with SOX proteins, BMP-2, or TGF,, showing good correspondence to the chondrogenic markers. Screening using the ATDC5-C2ER system identified several chondrogenic factors, including sorting nexin 19 (SNX19). SNX19 was expressed in the limb cartilage of mouse embryos and in the degraded cartilage of adult mouse knee joints during osteoarthritis progression. The gain-of-function and loss-of-function analyses revealed a potent chondrogenic activity of SNX19. Conclusion We established the ATDC5-C2ER system for efficient monitoring of chondrogenic differentiation by fluorescence analysis, and we identified a novel chondrogenic factor (SNX19) using this system. This system will be useful for elucidating the molecular network of chondrogenic differentiation. [source] The brachydactylies: a molecular disease familyCLINICAL GENETICS, Issue 2 2009S Mundlos Brachydactyly refers to shortening of the hands and/or feet due to missing, deformed, or shortened bones. It may occur as an isolated trait or as part of a syndrome. According to their pattern of skeletal involvement, the isolated brachydactyly forms have been categorized in the groups A,D including several subgroups. As in many other genetic conditions, there is considerable phenotypic overlap between the groups. The identification of the molecular causes of these conditions has offered insights into their pathogenesis. The generation of animal models has facilitated research on the pathogenic events during digit development that lead to the brachydactyly phenotype. These studies have shown that the BMP pathway plays a pivotal role in the normal development of digits and joints and that the majority of brachydactyly disease genes are directly or indirectly linked to this pathway. Together, these genes function in a regulatory network which is deregulated in the disease state. As a consequence of the close interactions within the network, overlapping phenotypes are generated that are, nevertheless, characterized by specific recognizable patterns. This principle does not only apply for the brachydactylies but is also valid for many other disease entities. Groups of diseases that show a common phenotypic pattern due to the deregulation of a molecular network are suggested to be called molecular disease families. [source] Expression survey of genes critical for tooth development in the human embryonic tooth germDEVELOPMENTAL DYNAMICS, Issue 5 2007Dahe Lin Abstract In the developing murine tooth, the expression patterns of numerous regulatory genes have been examined and their roles have begun to be revealed. To unveil the molecular mechanisms that regulate human tooth morphogenesis, we examined the expression patterns of several regulatory genes, including BMP4, FGF8, MSX1, PAX9, PITX2, and SHOX2, and compared them with that found in mice. All of these genes are known to play critical roles in murine tooth development. Our results show that these genes exhibit basically similar expression patterns in the human tooth germ compared with that in the mouse. However, slightly different expression patterns were also observed for some of the genes at certain stages. For example, MSX1 expression was detected in the inner enamel epithelium in addition to the dental mesenchyme at the bell stage of the human tooth. Moreover, FGF8 expression remained in the dental epithelium at the cap stage, while PAX9 and SHOX2 expression was detected in both dental epithelium and mesenchyme of the human tooth germ. Our results indicate that, although slight differences exist in the gene expression patterns, the human and mouse teeth not only share considerable homology in odontogenesis but also use similar underlying molecular networks. Developmental Dynamics 236:1307,1312, 2007. © 2007 Wiley-Liss, Inc. [source] Charting protein complexes, signaling pathways, and networks in the immune systemIMMUNOLOGICAL REVIEWS, Issue 1 2006Angela Bauch Summary:, Systematic deciphering of protein,protein interactions has the potential to generate comprehensive and instructive signaling networks and to fuel new therapeutic and diagnostic strategies. Here, we describe how recent advances in high-throughput proteomic technologies, involving biochemical purification methods and mass spectrometry analysis, can be applied systematically to the characterization of protein complexes and the computation of molecular networks. The networks obtained form the basis for further functional analyses, such as knockdown by RNA interference, ultimately leading to the identification of nodes that represent candidate targets for pharmacological exploitation. No individual experimental approach can accurately elucidate all critical modulatory components and biological aspects of a signaling network. Such functionally annotated protein,protein interaction networks, however, represent an ideal platform for the integration of additional datasets. By providing links between molecules, they also provide links to all previous observations associated with these molecules, be they of genetic, pharmacological, or other origin. As exemplified here by the analysis of the tumor necrosis factor (TNF)-,/nuclear factor-,B (NF-,B) signaling pathway, the approach is applicable to any mammalian cellular signaling pathway in the immune system. [source] Devil inside: does plant programmed cell death involve the endomembrane system?PLANT CELL & ENVIRONMENT, Issue 9 2010JEAN-LUC CACAS ABSTRACT Eukaryotic cells have to constantly cope with environmental cues and integrate developmental signals. Cell survival or death is the only possible outcome. In the field of animal biology, tremendous efforts have been put into the understanding of mechanisms underlying cell fate decision. Distinct organelles have been proven to sense a broad range of stimuli and, if necessary, engage cell death signalling pathway(s). Over the years, forward and reverse genetic screens have uncovered numerous regulators of programmed cell death (PCD) in plants. However, to date, molecular networks are far from being deciphered and, apart from the autophagic compartment, no organelles have been assigned a clear role in the regulation of cellular suicide. The endomembrane system (ES) seems, nevertheless, to harbour a significant number of cell death mediators. In this review, the involvement of this system in the control of plant PCD is discussed in-depth, as well as compared and contrasted with what is known in animal and yeast systems. [source] Discovering functions and revealing mechanisms at molecular level from biological networksPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 16 2007Shihua Zhang Abstract With the increasingly accumulated data from high-throughput technologies, study on biomolecular networks has become one of key focuses in systems biology and bioinformatics. In particular, various types of molecular networks (e.g., protein,protein interaction (PPI) network; gene regulatory network (GRN); metabolic network (MN); gene coexpression network (GCEN)) have been extensively investigated, and those studies demonstrate great potentials to discover basic functions and to reveal essential mechanisms for various biological phenomena, by understanding biological systems not at individual component level but at a system-wide level. Recent studies on networks have created very prolific researches on many aspects of living organisms. In this paper, we aim to review the recent developments on topics related to molecular networks in a comprehensive manner, with the special emphasis on the computational aspect. The contents of the survey cover global topological properties and local structural characteristics, network motifs, network comparison and query, detection of functional modules and network motifs, function prediction from network analysis, inferring molecular networks from biological data as well as representative databases and software tools. [source] Array-based proteomics: mapping of protein circuitries for diagnostics, prognostics, and therapy guidance in cancerTHE JOURNAL OF PATHOLOGY, Issue 5 2006C Gulmann Abstract The human proteome, due to the enormity of post-translational permutations that result in large numbers of isoforms, is much more complex than the genome and alterations in cancer can occur in ways that are not predictable by translational analysis alone. Proteomic analysis therefore represents a more direct way of investigating disease at the individual patient level. Furthermore, since most novel therapeutic targets are proteins, proteomic analysis potentially has a central role in patient care. At the same time, it is becoming clear that mapping entire networks rather than individual markers may be necessary for robust diagnostics as well as tailoring of therapy. Consequently, there is a need for high-throughput multiplexed proteomic techniques, with the capability of scanning multiple cases and analysing large numbers of endpoints. New types of protein arrays combined with advanced bioinformatics are currently being used to identify molecular signatures of individual tumours based on protein pathways and signalling cascades. It is envisaged that analysing the cellular ,circuitry' of ongoing molecular networks will become a powerful clinical tool in patient management. Copyright © 2006 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Identification of the core element responsive to runt-related transcription factor 2 in the promoter of human type x collagen geneARTHRITIS & RHEUMATISM, Issue 1 2009Akiro Higashikawa Objective Type X collagen and runt-related transcription factor 2 (RUNX-2) are known to be important for chondrocyte hypertrophy during skeletal growth and repair and development of osteoarthritis (OA) in mice. Aiming at clinical application, this study was undertaken to investigate transcriptional regulation of human type X collagen by RUNX-2 in human cells. Methods Localization of type X collagen and RUNX-2 was determined by immunohistochemistry, and their functional interaction was examined in cultured mouse chondrogenic ATDC-5 cells. Promoter activity of the human type X collagen gene (COL10A1) was examined in human HeLa, HuH7, and OUMS27 cells transfected with a luciferase gene containing a 4.5-kb promoter and fragments. Binding to RUNX-2 was examined by electrophoretic mobility shift assay and chromatin immunoprecipitation. Results RUNX-2 and type X collagen were co-localized in mouse limb cartilage and bone fracture callus. Gain and loss of function of RUNX-2 revealed that RUNX-2 is essential for type X collagen expression and terminal differentiation of chondrocytes. Human COL10A1 promoter activity was enhanced by RUNX-2 alone and more potently by RUNX-2 in combination with the coactivator core-binding factor , in all 3 human cell lines examined. Deletion, mutagenesis, and tandem repeat analyses identified the core responsive element as the region between ,89 and ,60 bp (termed the hypertrophy box [HY box]), which showed specific binding to RUNX-2. Other putative RUNX-2 binding motifs in the human COL10A1 promoter did not respond to RUNX-2 in human cells. Conclusion Our findings indicate that the HY box is the core element responsive to RUNX-2 in human COL10A1 promoter. Studies on molecular networks related to RUNX-2 and the HY box will lead to treatments of skeletal growth retardation, bone fracture, and OA. [source] Self-Assembled Monolayers of Alkoxy-Substituted Octadehydrodibenzo[12]annulenes on a Graphite Surface: Attempts at peri -Benzopolyacene Formation by On-Surface PolymerizationCHEMISTRY - A EUROPEAN JOURNAL, Issue 28 2010Kazukuni Tahara Dr. Abstract Self-assembled monolayers of a series of tetraalkoxy-substituted octadehydrodibenzo[12]annulene (DBA) derivatives 1,c,g possessing butadiyne linkages were studied at the 1,2,4-trichlorobenzene (TCB) or 1-phenyloctane/graphite interface by scanning tunneling microscopy (STM). The purpose of this research is not only to investigate the structural variation of two-dimensional (2D) monolayers, but also to assess a possibility for peri -benzopolyacene formation by two-dimensionally controlled polymerization on a surface. As a result, the formation of three structures, porous, linear, and lamella structures, were observed by changing the alkyl chain length and the solute concentration. The formation of multilayers of the lamella structure was often observed for all compounds. The selection of molecular networks is basically ascribed to intermolecular and molecule,substrate interactions per unit area and network density. The selective appearance of the linear structure of 1,d is attributed to favorable epitaxial registry matching between the substrate lattice and the overlayer lattice. Even though the closest interatomic distance between the diacetylenic units of the DBAs in the lamella structure (,0.6,nm) is slightly larger compared to the typical distances necessary for topochemical polymerization, the reactivity toward external stimuli (electronic-pulse irradiation from an STM tip and UV irradiation) was investigated. Unfortunately, no evidence for polymerization of the DBAs on the surface was observed. The present results indicate the necessity for further designing a suitable system for the on-surface construction of structurally novel conjugated polymers, which are otherwise difficult to prepare. [source] Fault Diagnosis Engineering in Molecular Signaling Networks: An Overview and Applications in Target DiscoveryCHEMISTRY & BIODIVERSITY, Issue 5 2010Ali Abdi Abstract Fault diagnosis engineering is a key component of modern industrial facilities and complex systems, and has gone through considerable developments in the past few decades. In this paper, the principles and concepts of molecular fault diagnosis engineering are reviewed. In this area, molecular intracellular networks are considered as complex systems that may fail to function, due to the presence of some faulty molecules. Dysfunction of the system due to the presence of a single or multiple molecules can ultimately lead to the transition from the normal state to the disease state. It is the goal of molecular fault diagnosis engineering to identify the critical components of molecular networks, i.e., those whose dysfunction can interrupt the function of the entire network. The results of the fault analysis of several signaling networks are discussed, and possible connections of the findings with some complex human diseases are examined. Implications of molecular fault diagnosis engineering for target discovery and drug development are outlined as well. [source] Steering Two-Dimensional Molecular Growth via Dipolar InteractionCHEMPHYSCHEM, Issue 12 2009Stefan Kuck Molecular networks: Chiral and metallized Salen molecules on a Cu(111) are investigated using local probe techniques (see figure). Whereas for the parent Co-Salen molecule no self-assembly is observed, in the metal,organic complexes the growth of large and regular molecular networks is achieved through a target-oriented synthetic design of the local electrostatic dipolar molecular fields. [source] | ||||||||||||||||